Enveomics collection

A toolbox for microbial genomics and metagenomics

BlastPairwise.AAsubs.pl

Counts the different AA substitutions in the best hit blast alignments, from a BLASTP pairwise format output (-outfmt 0 in BLAST+, -m 0 in legacy BLAST).

    See source code, Artistic license 2.0.

§ References

    Konstantinidis et al, 2009, AEM; Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

§ Usage

BlastPairwise.AAsubs.pl select in_file > out_file

§ Arguments

Cigar char*
 select  Use '+' for similar substitutions, use '_' for non similar substitutions.
Blast M0*
 in_file  Blast in 'pairwise text' format (-outfmt/-m 0).
AA subs*
 out_file  A tab-delimited raw file with one substitution per row and columns: (1) Name-of-query_Name-of-subject, (2) AA-in-subject, (3) AA-in-query, (4) Total-Align-Length.
* Mandatory.